Read in the indata.rds dataset. Which assays are
availble in this dataset. Print out the sample information data
(colData).
indata <- readRDS("~/Desktop/indata.rds") ## change directory information
### lists the availble gene expression types
assays(indata)
## List of length 4
## names(4): counts log_counts counts_cpm log_counts_cpm
### gene expression data
counts <- assay(indata, "counts")
#head(counts)
### sample information
colData(indata)
## DataFrame with 89 rows and 4 columns
## BMI Tb_status bmi_cat2 batch
## <numeric> <factor> <factor> <factor>
## 10200042B 14.81 LTBI mal 1
## 10200088B 13.92 LTBI mal 1
## 10200129B 24.15 LTBI well 1
## 10200131B 15.09 LTBI mal 1
## 10200171B 28.12 LTBI well 1
## ... ... ... ... ...
## 10200111A 16.5 LTBI well 2
## 10200112A 11.5 TB mal 2
## 10200016A 15.6 TB mal 2
## 10200015A 14.3 TB mal 2
## 10200087A 15.6 TB mal 2
Summarize the sample information data, provide relevant tables and plots.
column_dat <- as_tibble(colData(indata))
datatable(column_dat)
Evaluate whether batch effects are present in the data and if
correction if is needed. If so, correct for batch. Use the
log_counts_cpm assay for plotting.
Plot the first two principal components, colored by batch, TB status as symbols
log_cpm_dat <- as.matrix(assay(indata, "log_counts_cpm"))
Plot the UMAP projection, colored by batch, TB status as symbols
Adjust the log_counts_cpm with ComBat and the
counts using ComBat-Seq. Use Tb_status and
bmi_cat2 as covariates.
## ComBat on log_counts_cpm
cov_model <- model.matrix(~Tb_status+bmi_cat2,
data=colData(indata))
combat_adjust <- ComBat(log_cpm_dat, colData(indata)$batch, cov_model)
## Found2batches
## Adjusting for2covariate(s) or covariate level(s)
## Standardizing Data across genes
## Fitting L/S model and finding priors
## Finding parametric adjustments
## Adjusting the Data
assay(indata,"combat_log_counts_cpm") <- combat_adjust
## ComBat-Seq on counts
Plot the first two principal components, colored by batch, TB status as symbols
Plot the UMAP projection, colored by batch, TB status as symbols
set.seed(0)
Use DESeq2 to calculate differential expression using the ComBat-Seq
adjusted counts between TB and LTBI (Tb_status), adjusting
for malnutrition status (bmi_cat2).
# Make a Heatmap of DEGs
The TBSignatureProfiler was developed in the Johnson Lab in 2021 to profile new and existing TB gene expression signatures https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-05598-z. Help documentation and vignettes are available at https://wejlab.github.io/TBSignatureProfiler-docs/
TBsigs <- TBsignatures[-12] ## Remove Chendi_HIV_2 signature because we only have one of the genes
ssgsea_res <- runTBsigProfiler(indata, useAssay = "combat_log_counts_cpm",
signatures = TBsigs,
algorithm = "ssGSEA",
combineSigAndAlgorithm = TRUE,
parallel.sz = 1)
## Warning: Calling gsva(expr=., gset.idx.list=., method=., ...) is deprecated;
## use a method-specific parameter object (see '?gsva').
for (i in names(TBsigs)){
cat("#####" , i, "\n")
print(signatureBoxplot(ssgsea_res, name=i, signatureColNames = i,
annotationColName = c("Tb_status")))
cat("\n\n")
}
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## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
## Warning: Use of `boxplotdfm$Group` is discouraged.
## ℹ Use `Group` instead.
## Warning: Use of `boxplotdfm$Score` is discouraged.
## ℹ Use `Score` instead.
for (i in names(TBsigs)){
cat("#####" , i, "\n")
cat("\n\n")
}
set.seed(0)
set.seed(0)
for (i in names(TBsigs)){
cat("#####" , i, "\n")
cat("\n\n")
}